Starting phenix.real_space_refine on Thu May 15 05:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a65_11666/05_2025/7a65_11666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a65_11666/05_2025/7a65_11666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a65_11666/05_2025/7a65_11666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a65_11666/05_2025/7a65_11666.map" model { file = "/net/cci-nas-00/data/ceres_data/7a65_11666/05_2025/7a65_11666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a65_11666/05_2025/7a65_11666.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8075 2.51 5 N 2086 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12521 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 7.88, per 1000 atoms: 0.63 Number of scatterers: 12521 At special positions: 0 Unit cell: (102.48, 207.48, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2310 8.00 N 2086 7.00 C 8075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 53.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.705A pdb=" N PHE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 82 removed outlier: 4.504A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.693A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 158 removed outlier: 3.642A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 187 removed outlier: 4.128A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 4.292A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.708A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.697A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 269 through 323 removed outlier: 3.544A pdb=" N LEU A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 348 removed outlier: 4.036A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.680A pdb=" N ILE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.752A pdb=" N THR A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.810A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.585A pdb=" N LEU A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.653A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.822A pdb=" N THR A 591 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.522A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 699 through 706 removed outlier: 3.525A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 removed outlier: 3.914A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 741 removed outlier: 3.627A pdb=" N ALA A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 799 Processing helix chain 'A' and resid 800 through 806 removed outlier: 3.536A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 810 removed outlier: 3.573A pdb=" N THR A 810 " --> pdb=" O PRO A 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 810' Processing helix chain 'A' and resid 811 through 854 removed outlier: 3.647A pdb=" N LEU A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.638A pdb=" N THR A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 881 removed outlier: 3.600A pdb=" N ILE A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 903 removed outlier: 3.540A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 912 through 966 removed outlier: 4.582A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 4.457A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 995 removed outlier: 3.633A pdb=" N ALA A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 removed outlier: 3.625A pdb=" N ALA A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 4.246A pdb=" N VAL A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.968A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1160 Processing helix chain 'A' and resid 1163 through 1167 removed outlier: 3.996A pdb=" N THR A1167 " --> pdb=" O LYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.728A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 Processing helix chain 'A' and resid 1207 through 1222 removed outlier: 3.902A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.205A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1272 removed outlier: 3.535A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.593A pdb=" N SER B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.656A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.082A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 206 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.636A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 422 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA A 599 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 424 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE A 601 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 426 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1060 removed outlier: 5.167A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1115 removed outlier: 3.638A pdb=" N GLY A1114 " --> pdb=" O ILE A1196 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 14 Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.528A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 102 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.565A pdb=" N ASN B 142 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 removed outlier: 4.257A pdb=" N TRP B 153 " --> pdb=" O GLN B 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.812A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.635A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.635A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 160 731 hydrogen bonds defined for protein. 2085 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3974 1.34 - 1.46: 2940 1.46 - 1.58: 5788 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 12785 Sorted by residual: bond pdb=" C TYR A1087 " pdb=" N ASP A1088 " ideal model delta sigma weight residual 1.333 1.300 0.033 1.61e-02 3.86e+03 4.24e+00 bond pdb=" C ALA B 116 " pdb=" N ALA B 117 " ideal model delta sigma weight residual 1.339 1.246 0.093 5.57e-02 3.22e+02 2.81e+00 bond pdb=" C13 CLR A1303 " pdb=" C17 CLR A1303 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C10 CLR A1303 " pdb=" C9 CLR A1303 " ideal model delta sigma weight residual 1.551 1.518 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" CA ALA A 260 " pdb=" CB ALA A 260 " ideal model delta sigma weight residual 1.527 1.488 0.040 2.48e-02 1.63e+03 2.56e+00 ... (remaining 12780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 16659 1.77 - 3.54: 579 3.54 - 5.31: 84 5.31 - 7.08: 17 7.08 - 8.85: 4 Bond angle restraints: 17343 Sorted by residual: angle pdb=" N SER A1020 " pdb=" CA SER A1020 " pdb=" C SER A1020 " ideal model delta sigma weight residual 113.97 109.29 4.68 1.28e+00 6.10e-01 1.34e+01 angle pdb=" C VAL A1273 " pdb=" CA VAL A1273 " pdb=" CB VAL A1273 " ideal model delta sigma weight residual 111.71 108.72 2.99 8.50e-01 1.38e+00 1.24e+01 angle pdb=" N VAL A 592 " pdb=" CA VAL A 592 " pdb=" C VAL A 592 " ideal model delta sigma weight residual 112.96 109.75 3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" C TYR A1087 " pdb=" N ASP A1088 " pdb=" CA ASP A1088 " ideal model delta sigma weight residual 121.83 116.94 4.89 1.56e+00 4.11e-01 9.83e+00 angle pdb=" C SER B 68 " pdb=" N GLY B 69 " pdb=" CA GLY B 69 " ideal model delta sigma weight residual 122.73 119.95 2.78 9.30e-01 1.16e+00 8.91e+00 ... (remaining 17338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 7188 16.20 - 32.39: 536 32.39 - 48.59: 134 48.59 - 64.79: 34 64.79 - 80.98: 6 Dihedral angle restraints: 7898 sinusoidal: 3312 harmonic: 4586 Sorted by residual: dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N ILE B 56 " pdb=" CA ILE B 56 " ideal model delta harmonic sigma weight residual 180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN B 216 " pdb=" C ASN B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ARG B 217 " pdb=" C ARG B 217 " pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1656 0.059 - 0.119: 299 0.119 - 0.178: 39 0.178 - 0.237: 6 0.237 - 0.296: 6 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C13 CLR A1300 " pdb=" C12 CLR A1300 " pdb=" C14 CLR A1300 " pdb=" C17 CLR A1300 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C13 CLR A1305 " pdb=" C12 CLR A1305 " pdb=" C14 CLR A1305 " pdb=" C17 CLR A1305 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C13 CLR A1303 " pdb=" C12 CLR A1303 " pdb=" C14 CLR A1303 " pdb=" C17 CLR A1303 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2003 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 48 " 0.035 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 49 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 99 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 100 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C THR A 173 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 173 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 174 " -0.010 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1468 2.74 - 3.28: 12786 3.28 - 3.82: 20171 3.82 - 4.36: 23694 4.36 - 4.90: 40420 Nonbonded interactions: 98539 Sorted by model distance: nonbonded pdb=" O PHE A 623 " pdb=" OG1 THR A 627 " model vdw 2.200 3.040 nonbonded pdb=" O SER A1272 " pdb=" OG SER A1272 " model vdw 2.202 3.040 nonbonded pdb=" O PHE C 29 " pdb=" NH2 ARG C 72 " model vdw 2.218 3.120 nonbonded pdb=" O ALA A 233 " pdb=" OG SER A 237 " model vdw 2.218 3.040 nonbonded pdb=" O SER A 43 " pdb=" NZ LYS A 48 " model vdw 2.230 3.120 ... (remaining 98534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 12790 Z= 0.334 Angle : 0.789 8.845 17353 Z= 0.432 Chirality : 0.049 0.296 2006 Planarity : 0.004 0.052 2156 Dihedral : 12.706 80.982 4943 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.72 % Allowed : 7.72 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.19), residues: 1584 helix: -1.10 (0.16), residues: 759 sheet: -0.71 (0.29), residues: 283 loop : -2.42 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 160 HIS 0.004 0.001 HIS A 166 PHE 0.020 0.002 PHE B 94 TYR 0.024 0.002 TYR C 95 ARG 0.004 0.001 ARG A 798 Details of bonding type rmsd hydrogen bonds : bond 0.17741 ( 719) hydrogen bonds : angle 7.19739 ( 2085) SS BOND : bond 0.00773 ( 5) SS BOND : angle 1.62653 ( 10) covalent geometry : bond 0.00743 (12785) covalent geometry : angle 0.78791 (17343) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7992 (t60) cc_final: 0.7673 (t60) REVERT: A 499 GLU cc_start: 0.6276 (mt-10) cc_final: 0.6025 (mm-30) REVERT: A 514 MET cc_start: 0.5423 (mtm) cc_final: 0.4637 (tmm) REVERT: A 799 GLN cc_start: 0.7907 (mm110) cc_final: 0.7673 (mm-40) REVERT: A 816 THR cc_start: 0.7941 (m) cc_final: 0.7392 (t) REVERT: A 1183 ARG cc_start: 0.5891 (mtm180) cc_final: 0.5521 (mtp85) REVERT: A 1270 MET cc_start: -0.0551 (OUTLIER) cc_final: -0.0877 (mtt) REVERT: B 171 GLN cc_start: 0.8046 (tt0) cc_final: 0.6997 (tt0) REVERT: C 25 SER cc_start: 0.8624 (p) cc_final: 0.8135 (t) REVERT: C 121 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (ptmm) REVERT: C 173 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.7800 (Cg_exo) outliers start: 23 outliers final: 7 residues processed: 297 average time/residue: 0.2926 time to fit residues: 118.5098 Evaluate side-chains 159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 1270 MET Chi-restraints excluded: chain A residue 1271 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.0670 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 398 HIS A 438 GLN A 462 ASN A 475 GLN A 612 HIS A 704 ASN A 750 GLN A 799 GLN A 912 GLN A 914 GLN A 946 GLN A 966 HIS A1054 GLN A1105 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 HIS A1182 GLN A1248 ASN B 18 GLN B 129 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126206 restraints weight = 27492.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123304 restraints weight = 40113.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124216 restraints weight = 34475.620| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12790 Z= 0.139 Angle : 0.597 8.414 17353 Z= 0.309 Chirality : 0.042 0.159 2006 Planarity : 0.004 0.040 2156 Dihedral : 6.535 59.351 2131 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.70 % Allowed : 14.38 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1584 helix: 0.65 (0.18), residues: 787 sheet: 0.08 (0.31), residues: 276 loop : -1.92 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 698 HIS 0.004 0.001 HIS A 612 PHE 0.022 0.002 PHE A 200 TYR 0.016 0.001 TYR A1133 ARG 0.006 0.000 ARG A 538 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 719) hydrogen bonds : angle 5.01628 ( 2085) SS BOND : bond 0.00470 ( 5) SS BOND : angle 1.05089 ( 10) covalent geometry : bond 0.00282 (12785) covalent geometry : angle 0.59689 (17343) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7528 (mmm) cc_final: 0.7081 (tpp) REVERT: A 232 TRP cc_start: 0.7726 (t60) cc_final: 0.7304 (t60) REVERT: A 514 MET cc_start: 0.4777 (mtm) cc_final: 0.4280 (tmm) REVERT: A 616 MET cc_start: 0.1385 (mmp) cc_final: 0.0812 (mmm) REVERT: A 948 MET cc_start: 0.7480 (tpt) cc_final: 0.7269 (tpp) REVERT: A 949 MET cc_start: 0.8144 (tmm) cc_final: 0.7621 (tpt) REVERT: A 973 ASP cc_start: 0.8045 (t0) cc_final: 0.7673 (m-30) REVERT: A 1270 MET cc_start: 0.0243 (tpt) cc_final: -0.0425 (mtt) REVERT: C 173 PRO cc_start: 0.7697 (Cg_endo) cc_final: 0.7359 (Cg_exo) outliers start: 36 outliers final: 13 residues processed: 213 average time/residue: 0.2234 time to fit residues: 70.4482 Evaluate side-chains 154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1136 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2443 > 50: distance: 1 - 48: 27.356 distance: 8 - 51: 19.128 distance: 11 - 65: 29.077 distance: 42 - 48: 30.184 distance: 48 - 49: 30.087 distance: 49 - 50: 52.566 distance: 49 - 52: 64.608 distance: 50 - 51: 48.622 distance: 50 - 57: 56.183 distance: 52 - 53: 48.166 distance: 53 - 54: 15.054 distance: 54 - 55: 34.535 distance: 54 - 56: 30.605 distance: 58 - 59: 39.353 distance: 58 - 61: 17.811 distance: 59 - 60: 40.240 distance: 59 - 65: 43.105 distance: 61 - 62: 15.641 distance: 61 - 63: 46.500 distance: 62 - 64: 39.576 distance: 65 - 66: 9.901 distance: 66 - 67: 30.329 distance: 66 - 69: 29.969 distance: 67 - 68: 23.644 distance: 67 - 74: 52.261 distance: 69 - 70: 44.642 distance: 70 - 71: 29.152 distance: 71 - 72: 31.821 distance: 72 - 73: 26.551 distance: 74 - 75: 32.815 distance: 75 - 76: 9.542 distance: 75 - 78: 8.870 distance: 76 - 77: 7.216 distance: 76 - 85: 17.350 distance: 78 - 79: 22.536 distance: 79 - 80: 29.451 distance: 80 - 81: 15.344 distance: 81 - 82: 24.055 distance: 82 - 83: 27.303 distance: 82 - 84: 40.829 distance: 85 - 86: 5.107 distance: 86 - 87: 14.635 distance: 86 - 89: 27.811 distance: 87 - 88: 35.670 distance: 87 - 90: 61.100 distance: 90 - 91: 20.026 distance: 91 - 92: 55.186 distance: 91 - 94: 50.745 distance: 92 - 93: 25.625 distance: 92 - 98: 46.349 distance: 94 - 95: 49.594 distance: 95 - 96: 30.117 distance: 95 - 97: 28.716 distance: 98 - 99: 11.045 distance: 99 - 100: 50.095 distance: 99 - 102: 29.004 distance: 100 - 101: 25.968 distance: 103 - 104: 43.994 distance: 104 - 105: 36.217 distance: 104 - 107: 59.567 distance: 105 - 106: 41.353 distance: 105 - 108: 41.312 distance: 108 - 109: 39.506 distance: 109 - 110: 41.601 distance: 109 - 112: 45.633 distance: 110 - 111: 49.794 distance: 110 - 115: 32.423 distance: 112 - 113: 34.155 distance: 113 - 114: 69.134 distance: 115 - 116: 56.075 distance: 115 - 145: 36.220 distance: 116 - 117: 56.935 distance: 116 - 119: 43.809 distance: 117 - 122: 34.796 distance: 119 - 120: 37.682 distance: 119 - 121: 57.247